The campaign has been dominated by discussions on the ongoing peace talks with the leftist FARC rebel group.
President Juan Manuel Santos, who launched the negotiations in November 2012, lost the first round of the vote last month by a narrow margin.
His opponent Oscar Ivan Zuluaga says he will impose tougher conditions in order to carry on with the talks.
More than 32 million Colombians are eligible to vote, but the turnout was low in the first round at just over 40%.
Oscar Ivan Zuluaga, 55, is a former cabinet minister in Juan Manuel Santos’s centre-right government.
Their main disagreement seems to be on how to end a five-decade long conflict with Colombia’s main rebel group, the FARC.
Oscar Ivan Zuluaga initially said he would pull out of the talks and boost military attacks on the weakened rebel group.
That is the line adopted by his mentor, former president Alvaro Uribe, who was elected senator this year and is still one of the most influential figures in Colombian politics.
Later in the campaign he said he would continue to negotiate with the Farc provided the rebels renounced military action during the talks.
Juan Manuel Santos, 62, is aiming to conclude negotiations by the end of the year.
Government negotiators and rebel leaders have held several rounds of talks in the Cuban capital, Havana.
They have agreed on three points of the agenda drawn up in 2012: land reform, future political participation and drug trafficking, which is allegedly the main source of income for the rebels.
Three other points remain to be agreed on: the rights of the victims, disarmament of the rebels and the implementation of the agreement.
On the eve of the vote, Colombia stopped to watch the national team in its opening match in the football World Cup.
Both candidates were quick to congratulate the team on its 3-0 victory over Greece in the Brazilian city of Belo Horizonte.
Polls open at 08:00 local time and close at 16:00 local time. Results are expected shortly after polls close, as ballots are electronic.
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